net.sf.basedb.core
Class Scan

java.lang.Object
  net.sf.basedb.core.BasicItem<D>
      net.sf.basedb.core.OwnedItem<D>
          net.sf.basedb.core.SharedItem<D>
              net.sf.basedb.core.CommonItem<D>
                  net.sf.basedb.core.AnnotatedItem<ScanData>
                      net.sf.basedb.core.Scan

All Implemented Interfaces:

AccessControlled, Annotatable, Identifiable, Nameable, Ownable, Registered, Removable, Shareable

public class Scan
extends AnnotatedItem<ScanData>
implements Registered

A scan represents the scanning of a Hybridization by some scanner. A single hybridization may be scanned multiple times by the same or different scanner.

A single scan normally produces one or more Image:s which are analysed by some software to produce a RawBioAssay.

Version:

2.0

Author:

Nicklas

Last modified

$Date: 2009-04-06 14:52:39 +0200 (Mon, 06 Apr 2009) $

Field Summary

private boolean	protocolHasBeenSet
private boolean	scannerHasBeenSet
static Item	TYPE The type of item represented by this class.

Fields inherited from interface net.sf.basedb.core.Nameable

MAX_DESCRIPTION_LENGTH, MAX_NAME_LENGTH

Constructor Summary

Scan(ScanData data)

Method Summary

long	countImages() Counts all images that have been added to this scan.
long	countRawBioAssays() Counts all raw bioassays that have been created from this scan.
Set<Annotatable>	getAnnotatableParents() Get the hybridization.
ArrayDesign	getArrayDesign() Get the array design by connected to this scan following the hybridization to the array slide to the array batch to the array design.
static Scan	getById(DbControl dc, int id) Get a Scan object when you know the id.
Date	getEntryDate() Get the date that the item was registered in the database.
Hybridization	getHybridization() Get the Hybridization this scan is created from.
ItemQuery<Image>	getImages() Get a query that returns all images for this scan.
static Scan	getNew(DbControl dc, Hybridization hybridization) Create a new Scan item.
Protocol	getProtocol() Get the Protocol used to create this scan.
static ItemQuery<Scan>	getQuery() Get a query that returns scans.
ItemQuery<RawBioAssay>	getRawBioAssays() Get a query that returns all raw bioassays created from this scan.
Hardware	getScanner() Get the Hardware (scanner) used to create this scan.
Item	getType() Get the type of item represented by the object.
Set<ItemProxy>	getUsingItems() Get all: RawBioAssay:s created from this scan
boolean	isUsed() Check if: A RawBioAssay has been created from this scan
Image	newImage() Create a new Image for this scan.
RawBioAssay	newRawBioAssay(RawDataType rawDataType) Deprecated. Use RawBioAssay.getNew(DbControl, Platform, RawDataType) or RawBioAssay.getNew(DbControl, PlatformVariant, RawDataType) instead
void	setHybridization(Hybridization hybridization) Set the ArraySlide this hybridization is using.
(package private) void	setProjectDefaults(Project activeProject) Set scanner and protocol from project default settings.
void	setProtocol(Protocol protocol) Set the Protocol used to create this scan.
void	setScanner(Hardware scanner) Set the Hardware (scanner) used to create this scan.

Methods inherited from class net.sf.basedb.core.AnnotatedItem

getAnnotationSet, isAnnotated, removeAnnotations, toTransferable

Methods inherited from class net.sf.basedb.core.CommonItem

getDescription, getName, isRemoved, setDescription, setName, setRemoved, toTransferable

Methods inherited from class net.sf.basedb.core.SharedItem

getItemKey, getProjectKey, initPermissions, isShared, onBeforeCommit, setItemKey, setProjectKey, toTransferable

Methods inherited from class net.sf.basedb.core.OwnedItem

getOwner, isOwner, setOwner, takeOwnership, toTransferable

Methods inherited from class net.sf.basedb.core.BasicItem

addUsingItems, addUsingItems, checkPermission, equals, getData, getDbControl, getId, getPermissions, getPluginPermissions, getSessionControl, getVersion, hashCode, hasPermission, isDetached, isInDatabase, onAfterCommit, onAfterInsert, onRollback, setDbControl, toString, toTransferable, validate

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface net.sf.basedb.core.Identifiable

getId, getVersion

Methods inherited from interface net.sf.basedb.core.AccessControlled

checkPermission, getPermissions, hasPermission

Methods inherited from interface net.sf.basedb.core.Ownable

getOwner, isOwner, setOwner, takeOwnership

Field Detail

TYPE

public static final Item TYPE

The type of item represented by this class.

See Also:

Item.SCAN, getType()

scannerHasBeenSet

private boolean scannerHasBeenSet

protocolHasBeenSet

private boolean protocolHasBeenSet

Constructor Detail

Scan

Scan(ScanData data)

Method Detail

getNew

public static Scan getNew(DbControl dc,
                          Hybridization hybridization)
                   throws PermissionDeniedException,
                          BaseException

Create a new Scan item.

Parameters:

dc - The DbControl which will be used for permission checking and database access

hybridization - The hybridization the scan originates from

Returns:

The new Scan item

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for the hybridization

BaseException - If there is an error

getById

public static Scan getById(DbControl dc,
                           int id)
                    throws ItemNotFoundException,
                           PermissionDeniedException,
                           BaseException

Get a Scan object when you know the id.

Parameters:

dc - The DbControl which will be used for permission checking and database access.

id - The id of the item to load

Returns:

The Scan item

Throws:

ItemNotFoundException - If an item with the specified id is not found

PermissionDeniedException - If the logged in user doesn't have read permission to the item

BaseException - If there is another error

getQuery

public static ItemQuery<Scan> getQuery()

Get a query that returns scans.

Returns:

An ItemQuery object

getType

public Item getType()

Description copied from interface: Identifiable

Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.

Specified by:

getType in interface Identifiable

Returns:

A value indicating the type of item

getAnnotatableParents

public Set<Annotatable> getAnnotatableParents()
                                       throws BaseException

Get the hybridization.

Specified by:

getAnnotatableParents in interface Annotatable

Returns:

A set containing annotatable items, or null

Throws:

BaseException - If there is an error

getEntryDate

public Date getEntryDate()

Description copied from interface: Registered

Get the date that the item was registered in the database.

Specified by:

getEntryDate in interface Registered

Returns:

A date or null if this is not known

isUsed

public boolean isUsed()
               throws BaseException

Check if:

• A RawBioAssay has been created from this scan

Overrides:

isUsed in class BasicItem<ScanData>

Returns:

TRUE if this item is used, FALSE otherwise

Throws:

BaseException - If not able to tell if item is used or not.

See Also:

BasicItem.getUsingItems()

getUsingItems

public Set<ItemProxy> getUsingItems()

Get all:

• RawBioAssay:s created from this scan

  Overrides:

  getUsingItems in class BasicItem<ScanData>

  Returns:

  A set containing proxies for the items, or an empty set if no items are using this item

  Since:

  2.2

  See Also:

  BasicItem.addUsingItems(Set, Item, org.hibernate.Query)

setProjectDefaults

void setProjectDefaults(Project activeProject)
                  throws BaseException

Set scanner and protocol from project default settings.

Overrides:

setProjectDefaults in class BasicItem<ScanData>

Parameters:

activeProject - The currently active project

Throws:

BaseException

Since:

2.9

getHybridization

public Hybridization getHybridization()
                               throws PermissionDeniedException,
                                      BaseException

Get the Hybridization this scan is created from. A scan must always have a hybridization.

Returns:

The Hybridization item

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the hybridization

BaseException - If there is another error.

setHybridization

public void setHybridization(Hybridization hybridization)
                      throws InvalidDataException,
                             PermissionDeniedException

Set the ArraySlide this hybridization is using.

Parameters:

hybridization - The hybridization, null is not allowed

Throws:

InvalidDataException - If the hybridization is null

PermissionDeniedException - If the logged in user doesn't have write permission for the scan use permission for the hybridization

BaseException - If there is another error

getScanner

public Hardware getScanner()
                    throws PermissionDeniedException,
                           BaseException

Get the Hardware (scanner) used to create this scan.

Returns:

The Hardware item or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the scanner

BaseException - If there is another error.

setScanner

public void setScanner(Hardware scanner)
                throws PermissionDeniedException

Set the Hardware (scanner) used to create this scan.

Parameters:

scanner - The scanner or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the scan use permission for the scanner

BaseException - If there is another error

getProtocol

public Protocol getProtocol()
                     throws PermissionDeniedException,
                            BaseException

Get the Protocol used to create this scan.

Specified by:

getProtocol in interface Annotatable

Overrides:

getProtocol in class AnnotatedItem<ScanData>

Returns:

The Protocol item or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the protocol

BaseException - If there is another error.

setProtocol

public void setProtocol(Protocol protocol)
                 throws PermissionDeniedException

Set the Protocol used to create this scan.

Parameters:

protocol - The protocol or null if not known

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission for the scan use permission for the protocol

BaseException - If there is another error

getArrayDesign

public ArrayDesign getArrayDesign()
                           throws PermissionDeniedException,
                                  BaseException

Get the array design by connected to this scan following the hybridization to the array slide to the array batch to the array design.

Returns:

The array design, or null if no array design is connected

Throws:

PermissionDeniedException - If the logged in user doesn't have read permission for the array design

BaseException - If there is another error.

newRawBioAssay

public RawBioAssay newRawBioAssay(RawDataType rawDataType)
                           throws PermissionDeniedException,
                                  BaseException

Deprecated. Use RawBioAssay.getNew(DbControl, Platform, RawDataType) or RawBioAssay.getNew(DbControl, PlatformVariant, RawDataType) instead

Create a new RawBioAssay from this scan.

Parameters:

rawDataType - The raw data type of the new bioassay

Returns:

The new RawBioAssay item

Throws:

PermissionDeniedException - If the logged in user doesn't have use permission for the scan

BaseException - If there is another error

getRawBioAssays

public ItemQuery<RawBioAssay> getRawBioAssays()

Get a query that returns all raw bioassays created from this scan.

Returns:

An ItemQuery object

countRawBioAssays

public long countRawBioAssays()
                       throws BaseException

Counts all raw bioassays that have been created from this scan. The count includes raw bioassays that the logged in user doesn't have access to.

Returns:

The number of raw bioassays

Throws:

BaseException - If the raw bioassays couldn't be counted.

newImage

public Image newImage()
               throws PermissionDeniedException,
                      BaseException

Create a new Image for this scan.

Returns:

The new Image item

Throws:

PermissionDeniedException - If the logged in user doesn't have write permission

BaseException - If there is another error

getImages

public ItemQuery<Image> getImages()

Get a query that returns all images for this scan.

Returns:

An ItemQuery object

countImages

public long countImages()
                 throws BaseException

Counts all images that have been added to this scan. The count includes images that the logged in user doesn't have access to.

Returns:

The number of images

Throws:

BaseException - If the images couldn't be created.